Identification of putative miR direct targets
Glioblastoma Multiforme (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
Maintained by Sachet Shukla (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Identification of putative miR direct targets. Broad Institute of MIT and Harvard. doi:10.7908/C10G3HSJ
Overview
Introduction

This pipeline infers putative direct gene targets of miRs based on miR and gene expression profiles across multiple samples.

Summary

This pipeline use a relevance network approach to infer putative miR:mRNA regulatory connections. All miR:mRNA pairs that have correlations < -0.3 and have predicted interactions in three sequence prediction databases (Miranda, Pictar, Targetscan) define the final network.

Results
Overlap of miR:gene network with sequence prediction databases

Figure 1.  Get High-res Image Distribution of miR:gene pairs by the number of sequence prediction databases that predict an interaction between the two molecules. Miranda, Targetscan and Pictar are the three databases used in the analysis. Only miR:gene pairs that have correlation values less than the threshold are shown.

miR connectivity distribution

Figure 2.  Get High-res Image Summary of miR counts by the number of associated genes in the putative direct target network

Gene connectivity distribution

Figure 3.  Get High-res Image Summary of gene counts by the number of associated miRs in the putative direct target network

Significant miR:gene edges

Table 1.  Get Full Table List of miR:gene pairs with corr < -0.30 and prediction support in Miranda, Targetscan and Pictar

miR gene corr prediction databases miranda pictar targetscan total
hsa-mir-22 CHD7 -0.5 miranda,pictar,targetscan 1 1 1 3
hsa-mir-34a SOX4 -0.47 miranda,pictar,targetscan 1 1 1 3
hsa-mir-27a FAM77C -0.46 miranda,pictar,targetscan 1 1 1 3
hsa-mir-23a PAK3 -0.44 miranda,pictar,targetscan 1 1 1 3
hsa-mir-9 FBN1 -0.43 miranda,pictar,targetscan 1 1 1 3
hsa-mir-152 CHD7 -0.43 miranda,pictar,targetscan 1 1 1 3
hsa-mir-34a DPYSL4 -0.43 miranda,pictar,targetscan 1 1 1 3
hsa-mir-27a CDK5R1 -0.42 miranda,pictar,targetscan 1 1 1 3
hsa-mir-9 P4HA2 -0.42 miranda,pictar,targetscan 1 1 1 3
hsa-mir-9 TGFBI -0.41 miranda,pictar,targetscan 1 1 1 3
miR connections

Table 2.  Get Full Table All miR hubs with their associated genes in the putative direct target network.

Mir Number.of.Genes Genes
hsa-mir-29a 21 ARVCF, BACH2, BCL11A, BLMH, DNMT3A, DNMT3B, EPHB3, HMGCS1, JARID1B, KCTD15, MYBL2, NASP, REV3L, RNF138, SOX12, SS18L1, TDG, TUBB, VASH2, ZBTB5,SETDB1
hsa-mir-9 17 ANXA2, CAPZA1, CAST, COL15A1, DSE, FBN1, GPR124, LDLRAP1, LEPRE1, P4HA2, RAI14, SHC1, SLC10A3, SLC25A24, TGFBI, TXNDC5,SDC2
hsa-mir-27a 13 AMOTL2, CA10, CABP1, CDK5R1, CHD7, EYA1, FAM77C, FRS3, PASK, PLCL2, RNF144A, SLCO5A1,RPS6KA5
hsa-mir-22 10 CHD7, CUL3, DGKI, H3F3A, JARID2, POGK, RSBN1, SNRK, SPEN,SEPHS1
hsa-mir-29b 10 BACH2, BLMH, DNMT3A, DNMT3B, JARID1B, MYBL2, TDG, TUBB, VASH2,NASP
hsa-mir-23a 9 B3GALT2, CDK5R1, CHD7, DNM3, MTSS1, PAK3, PKP4, SATB1,CAMTA1
hsa-mir-34a 7 E2F3, HN1, PDGFRA, SATB1, SOX4, TAF5,DPYSL4
hsa-mir-29c 5 BLMH, JARID1B, MYBL2, TUBB,BACH2
hsa-mir-155 4 CHD7, SATB1, ZNF238,CAMTA1
hsa-mir-222 4 POGZ, RIMS3, SHANK2,RP11-35N6.1
Gene connections

Table 3.  Get Full Table All gene hubs with their associated miRs in the putative direct target network.

Gene Number.of.Mirs Mirs
CHD7 5 hsa-mir-155, hsa-mir-22, hsa-mir-23a, hsa-mir-27a,hsa-mir-152
BLMH 3 hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
TUBB 3 hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
CDK5R1 3 hsa-mir-23a, hsa-mir-27a,hsa-mir-152
MYBL2 3 hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
JARID1B 3 hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
SATB1 3 hsa-mir-23a, hsa-mir-34a,hsa-mir-155
BACH2 3 hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
TDG 2 hsa-mir-29b,hsa-mir-29a
NASP 2 hsa-mir-29b,hsa-mir-29a
Methods & Data
Input

This section should list the files that were used as input.

  • Level 3 miR expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/8016774/GDAC_MergeDataFiles_5131616/GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt

  • Level 3 gene expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/8016781/GDAC_MergeDataFiles_4396203/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • miR:gene predicted interactions file = /xchip/cga/reference/miR_predictions/human_interactions.predicted.v2.txt

  • Miranda = microrna.org Aug 2010 release, Microcosm version 5

  • Pictar = version 1

  • Targetscan = release 5.2

Method

Pairwise Pearson correlations coefficients between all miR:gene pairs are first computed. All genes that have correlation values less than the user-defined threshold (-0.3) with a particular miR and have been predicted as targets of that miR in three sequence based prediction databases: Miranda[1][2] Pictar[3][4], TargetScan [5][6][7] are identified as putative direct targets of that miR. We infer a direct target miR:gene network which comprises all such putative direct associations.

  • threshold = -0.3

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
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[3] Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, Piedade ID, Gunsalus KC, Stoffel M, Rajewsky N, Combinatorial microRNA target predictions, Nature Genetics 37:495-500 (2005)
[4] Chen K, Rajewsky N, Natural selection on human microRNA binding sites inferred from SNP data., Nat Genet 38:1452-1456 (2006)
[5] Lewis BP, Burge CB, Bartel DP, Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets., Cell 120(120):15-20 (2005)
[6] Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP, MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing., Molecular Cell 27:91-105 (2007)
[7] Friedman RC, Farh KK, Burge CB, Bartel DP, Most Mammalian mRNAs Are Conserved Targets of MicroRNAs., Genome Research 19:92-105 (2009)